single-cell-bioinformatics

Course material in notebook format for learning about single cell bioinformatics methods. To view this material, you have several options:

1. View the live version

Where you can run and edit code (also accessible by clicking the pink "launch binder" badge above)

2. View the static version

Where you cannot run or edit code, but view all the content

3. Set this up on your own computer

• 0. If you're using Windows, install git
• 1. Install Miniconda with Python 3. Command line instructions for mac and linux are shown below.

# Mac OS X
curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh > miniconda.sh

# 64-bit Linux
curl https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh > miniconda.sh

# After downloading, install (both Mac and Linux)
bash -b miniconda.sh

• 2. Clone this repository and all submodules

git clone --recursive https://github.com/YeoLab/single-cell-bioinformatics

• 3. Go to the new directory

cd single-cell-bioinformatics

• 4. Create a new environment with the necessary packages

conda create --yes -n single-cell-bioinformatics --file conda_requirements.txt

• 5. Activate the environment

source activate single-cell-bioinformatics  # On windows, do "activate single-cell-bioinformatics"

• 6. Install the remaiing requirements

pip install -r requirements.txt

• 7. PHEW. Now you can launch the notebooks!!

jupyter notebook

Frozen versions of previous implementations

• SCRM 2016